3EHE | pdb_00003ehe

Crystal structure of UDP-glucose 4 epimerase (galE-1) from Archaeoglobus fulgidus

PDB DOI: https://doi.org/10.2210/pdb3EHE/pdb

Classification: ISOMERASE
Organism(s): Archaeoglobus fulgidus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-09-12 Released: 2008-10-14
Deposition Author(s): Agarwal, R., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.87 Å
R-Value Free:
0.287 (Depositor), 0.288 (DCC)
R-Value Work:
0.253 (Depositor), 0.253 (DCC)
R-Value Observed:
0.253 (Depositor)

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Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of galE-1 from Archaeoglobus fulgidus

Agarwal, R., Burley, S.K., Swaminathan, S.

To be published.

Macromolecule Content

Total Structure Weight: 71.87 kDa
Atom Count: 4,863
Modeled Residue Count: 580
Deposited Residue Count: 626
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-glucose 4-epimerase (GalE-1)	A, B	313	Archaeoglobus fulgidus	Mutation(s): 0 Gene Names: AF_0361
UniProt
Find proteins for O29886 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)) Explore O29886 Go to UniProtKB: O29886
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O29886
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.87 Å
R-Value Free: 0.287 (Depositor), 0.288 (DCC)
R-Value Work: 0.253 (Depositor), 0.253 (DCC)
R-Value Observed: 0.253 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.574	α = 90
b = 55.529	β = 97.52
c = 89.634	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
SHELXD	phasing
SHARP	phasing
ARP/wARP	model building
Coot	model building
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2008-10-14

Deposition Author(s):

Swaminathan, S.

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2008-10-14
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2021-02-10
Changes: Database references, Derived calculations, Structure summary
Version 1.4: 2024-02-21
Changes: Data collection, Database references

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.